The island of Cyprus was a historical endemic area for cystic echinococcosis (CE) in the Mediterranean. During the last decades, Cyprus has been an open-air laboratory and a model for testing and implementing control measures aiming to eliminate CE as a public health problem. Despite control and surveillance measures implemented during last 50 years, molecular characterization of Echinococcus granulosus sensu lato specimens has been never provided. In February 2023, the carcass of a stray dog collected in the Nicosia district was examined by the Veterinary Services and found infected with Echinococcus spp. worms. The worms were sent to the European Union Reference Laboratory (EURLP) for species/genotype identification. The sequences analyses of nad2 and nad5 genes allowed us to identify the tapeworms as Echinococcus canadensis, genotype G7b. In November 2023, a parasitic liver cyst was observed during the post-mortem examination of a mouflon from the same area of the dog's finding. The cyst sample was also referred to EURLP for identification and comparison with tapeworms previously collected from the dog. The sequences analysis of cox1 gene allowed to identify the cyst as E. granulosus sensu stricto, genotype G1. The finding of 2 different species of E. granulosus s.l. in a limited area raises epidemiological questions on the origin of the samples: whether distinct transmission cycles are present or a recent introduction event have occurred. From a public health perspective, it will be essential to conduct further molecular epidemiology studies to clarify the recent transmission dynamics of Echinococcus species in Cyprus.